Twenty-seven independent polymorphic protein loci including 2 very recently identified were detected by two-dimensional elecrophoresis of serum, erythrocyte, and fibroblast samples from individuals in two large pedigrees. The genetic basis of these protein variants was corroborated by their mendelian inheritance patterns, and by their quantitative gene dosage dependence. These protein polymorphisms should prove useful for genetic screening of families with genetic diseases. Disease associated proteins (apparent pI 5.1 and 5.2, and MW of 29k and 26k respectively) have been found in the cerebrospinal fluid of 21 patients (100%) with Creutzfeldt-Jakob disease (CJD). Of 18 other CNS diseases studied only spinal fluid from herpes simplex encephalitis (HSE) patients (50%) displayed similar proteins. Two other disease associated proteins (apparent pI 5.7 and 5.9, with a MW of 40k for both proteins) have been observed in the spinal fluids of patients with: CJD (67%), HSE (32%), multiple sclerosis (13%), Parkinson's Disease (12%), and schizophrenia (32%). Observation of these disease associated and polymorphic proteins was facilitated by the use of sensitive silver staining methods, introduced by this section, for the detection and quantitation of proteins separated on polyacrylamide gels. These staining methods continue to be refined, with sensitivity currently at the .01 ng level.